How to use the cameo.core.target.ReactionKnockinTarget function in cameo

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github biosustain / cameo / tests / test_targets.py View on Github external
def test_reaction_knock_in_target(self, model):
        reaction = Reaction(id="atpzase", name="Cosmic ATP generator")
        atp_z = Metabolite(id="atp_z", name="Cosmic ATP", compartment="c")

        reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
        knockin_target = ReactionKnockinTarget("atpzase", reaction)
        with model:
            knockin_target.apply(model)
            assert atp_z in model.metabolites
            assert reaction in model.reactions

        assert atp_z not in model.metabolites
        assert reaction not in model.reactions
github biosustain / cameo / tests / test_targets.py View on Github external
ki_target = ReactionKnockinTarget("a", None)

        ensemble_1 = EnsembleTarget("a", [modulation_target, ki_target])
        ensemble_2 = EnsembleTarget("a", [ki_target, modulation_target])

        assert ensemble_1.targets == ensemble_2.targets

        modulation_target = ReactionModulationTarget("b", 1, 0)
        swap_target = ReactionCofactorSwapTarget("b", [("nad_c", "nadh_c"), ("nadp_c", "nadph_c")])

        ensemble_1 = EnsembleTarget("b", [modulation_target, swap_target])
        ensemble_2 = EnsembleTarget("b", [swap_target, modulation_target])

        assert ensemble_1.targets == ensemble_2.targets

        ki_target = ReactionKnockinTarget("c", None)
        modulation_target = ReactionModulationTarget("c", 1, 0)
        swap_target = ReactionCofactorSwapTarget("c", [("nad_c", "nadh_c"), ("nadp_c", "nadph_c")])

        ensemble = EnsembleTarget("c", [modulation_target, swap_target, ki_target])
        assert ensemble.targets[0] == ki_target
        assert ensemble.targets[1] == swap_target
        assert ensemble.targets[2] == modulation_target
github biosustain / cameo / tests / test_core_strain_design.py View on Github external
def test_add_strain_design(self, cad_reaction):
        t1 = ReactionKnockoutTarget('PGI')
        t2 = ReactionKnockoutTarget('GAPD')
        t3 = ReactionKnockinTarget("CAD", cad_reaction)

        strain_design1 = StrainDesign([t1, t2, t3])

        t4 = ReactionModulationTarget("PGI", 5, 1)

        strain_design2 = StrainDesign([t4])

        with pytest.raises(IncompatibleTargets):
            strain_design1.__add__(strain_design2)
        with pytest.raises(IncompatibleTargets):
            strain_design2.__add__(strain_design1)

        with pytest.raises(IncompatibleTargets):
            strain_design1.__iadd__(strain_design2)
        with pytest.raises(IncompatibleTargets):
            strain_design2.__iadd__(strain_design1)
github biosustain / cameo / tests / test_targets.py View on Github external
with pytest.raises(IncompatibleTargets):
            EnsembleTarget("a", [ko_target, ki_target])
        with pytest.raises(IncompatibleTargets):
            EnsembleTarget("a", [ki_target, ko_target])

        ko_target = ReactionKnockoutTarget("b")
        swap_target = ReactionCofactorSwapTarget("b", [("nad_c", "nadh_c"), ("nadp_c", "nadph_c")])

        with pytest.raises(IncompatibleTargets):
            EnsembleTarget("b", [ko_target, swap_target])
        with pytest.raises(IncompatibleTargets):
            EnsembleTarget("b", [swap_target, ko_target])

        modulation_target = ReactionModulationTarget("c", 0, 0)
        ki_target = ReactionKnockinTarget("c", None)

        with pytest.raises(IncompatibleTargets):
            EnsembleTarget("c", [modulation_target, ki_target])
        with pytest.raises(IncompatibleTargets):
            EnsembleTarget("c", [ki_target, modulation_target])
github biosustain / cameo / tests / test_targets.py View on Github external
def test_gnomic_integration_ReactionKnockinTarget(self, model):
        reaction = Reaction(id="atpzase", name="Cosmic ATP generator")
        atp_z = Metabolite(id="atp_z", name="Cosmic ATP", compartment="c")

        reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
        knockin_target = ReactionKnockinTarget("atpzase", reaction)
        knockin_target_gnomic = knockin_target.to_gnomic()
        assert genotype_to_string(Genotype([knockin_target_gnomic])) == "+reaction.atpzase"

        reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
        knockin_target = ReactionKnockinTarget("atpzase", reaction, accession_id='atpzase', accession_db='unicorn')
        knockin_target_gnomic = knockin_target.to_gnomic()
        assert genotype_to_string(Genotype([knockin_target_gnomic])) == "+reaction.atpzase#unicorn:atpzase"
github biosustain / cameo / cameo / strain_design / pathway_prediction / pathway_predictor.py View on Github external
targets = DictList()
        for reaction in self.reactions:
            reaction = self._replace_adapted_metabolites(reaction)
            if reaction.id in metanetx.mnx2all:
                target = ReactionKnockinTarget(reaction.id, reaction, accession_id=reaction.id, accession_db='metanetx')
            else:
                target = ReactionKnockinTarget(reaction.id, reaction)
            targets.append(target)

        for reaction in self.exchanges:
            reaction = self._replace_adapted_metabolites(reaction)
            targets.append(ReactionKnockinTarget(reaction.id, reaction))

        product = self._replace_adapted_metabolites(self.product)
        product.lower_bound = 0
        targets.append(ReactionKnockinTarget(product.id, product))

        return targets
github biosustain / cameo / cameo / strain_design / pathway_prediction / pathway_predictor.py View on Github external
def _build_targets(self):
        targets = DictList()
        for reaction in self.reactions:
            reaction = self._replace_adapted_metabolites(reaction)
            if reaction.id in metanetx.mnx2all:
                target = ReactionKnockinTarget(reaction.id, reaction, accession_id=reaction.id, accession_db='metanetx')
            else:
                target = ReactionKnockinTarget(reaction.id, reaction)
            targets.append(target)

        for reaction in self.exchanges:
            reaction = self._replace_adapted_metabolites(reaction)
            targets.append(ReactionKnockinTarget(reaction.id, reaction))

        product = self._replace_adapted_metabolites(self.product)
        product.lower_bound = 0
        targets.append(ReactionKnockinTarget(product.id, product))

        return targets
github biosustain / cameo / cameo / strain_design / pathway_prediction / pathway_predictor.py View on Github external
def _build_targets(self):
        targets = DictList()
        for reaction in self.reactions:
            reaction = self._replace_adapted_metabolites(reaction)
            if reaction.id in metanetx.mnx2all:
                target = ReactionKnockinTarget(reaction.id, reaction, accession_id=reaction.id, accession_db='metanetx')
            else:
                target = ReactionKnockinTarget(reaction.id, reaction)
            targets.append(target)

        for reaction in self.exchanges:
            reaction = self._replace_adapted_metabolites(reaction)
            targets.append(ReactionKnockinTarget(reaction.id, reaction))

        product = self._replace_adapted_metabolites(self.product)
        product.lower_bound = 0
        targets.append(ReactionKnockinTarget(product.id, product))

        return targets